Methods and apparatus for cell culture array

ABSTRACT

Methods and systems are described for improved handling and/or culturing and/or assaying of cells, chemically active beads, or similar materials in microfluidic systems and microfluidic culture arrays.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a division of U.S. patent application Ser. No.11/994,997 filed on Aug. 11, 2008, incorporated herein by reference inits entirety, which is a 35 U.S.C. § 371 national stage completion of,and claims priority to, PCT international application numberPCT/US2006/026364 filed on Jul. 6, 2006, incorporated herein byreference in its entirety, which claims priority to, and the benefit of,U.S. provisional patent application Ser. No. 60/773,467 filed on Feb.14, 2006, incorporated herein by reference in its entirety, and whichalso claims priority to, and the benefit of, U.S. provisional patentapplication Ser. No. 60/697,449 filed on Jul. 7, 2005, incorporatedherein by reference in its entirety. Priority is claimed to each of theforegoing applications.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with Government support under N00014-03-1-0808,awarded by the Office of Naval Research, and under BES-0239333, awardedby the National Science Foundation. The Government has certain rights inthe invention.

COPYRIGHT NOTICE

Pursuant to 37 C.F.R. 1.71(e), applicants note that a portion of thisdisclosure contains material that is subject to copyright protection(such as, but not limited to, diagrams, device photographs, or any otheraspects of this submission for which copyright protection is or may beavailable in any jurisdiction). The copyright owner has no objection tothe facsimile reproduction by anyone of the patent document or patentdisclosure, as it appears in the Patent and Trademark Office patent fileor records, but otherwise reserves all copyright rights whatsoever.

FIELD OF THE INVENTION

The invention in specific embodiments relates generally to molecular andcellular sample preparation and/or culturing and/or analysis and moreparticularly to micro structures useful therewith. In further specificembodiments, the invention involves methods, systems, and/or devices forculturing and/or assaying cells and/or other biologically or chemicallyactive materials using a novel culture structure, array, method orchamber. In other embodiments, the present invention relates to methodsand/or system and/or apparatus enabling the culturing of cells in aconfiguration allowing for simulating living tissues and/or organsand/or solid tumors, such as systems for an artificial liver, kidney,pancreas, thyroid, etc. In specific embodiments, the invention involvesmethods and/or system and/or apparatus involving various structures formanipulating objects, such as cells or beads, in a fluidic medium andoptionally performing certain analysis or observations thereof orderiving materials produced from biologic cultures.

BACKGROUND OF THE INVENTION

The discussion of any work, publications, sales, or activity anywhere inthis submission, including in any documents submitted with thisapplication, shall not be taken as an admission that any such workconstitutes prior art. The discussion of any activity, work, orpublication herein is not an admission that such activity, work, orpublication existed or was known in any particular jurisdiction.

High quality molecular and cellular sample preparations are thefoundation for effective technology validation as well as for meaningfulbiological and clinical research and for various clinical and otherapplications. In vitro samples that closely represent their in vivocharacteristics could potentially benefit a wide range of molecular andcellular applications. Handling, characterization, culturing, andvisualization of cells or other biologically or chemically activematerials (such as beads coated with various biological molecules) hasbecome increasingly valued in the fields of drug discovery, diseasediagnoses and analysis, and a variety of other therapeutic andexperimental work.

Mammalian cell culture is an essential aspect of medical and biologicalresearch and development and ultimately treatment. However, most currentpractices are labor/resource intensive, not amenable to process control,cannot address cellular length scales, and prevent long-term continuousreal-time monitoring or observation. Furthermore, current cell culturepractices have not provided fully satisfactory solutions to thechallenges of maintaining effective solid aggregates of cells inculture.

Advances have been made by combining microfabrication and microfluidictechnologies with cell culture during the past decade; nevertheless,there is not yet a compact device effectively providing the samefunctionality as traditional cell culture.

Some recent publications and/or patent documents that discuss variousstrategies related to cell culture using microfluidic systems andrelated activities include the following U.S. patent applications andnon-patent literature, which, along with all citations therein, areincorporated herein by reference to provide background. A listing ofthese references here does not indicate the references constitute priorart.

Cytoplex, Inc. U.S. Pat. No. 6,653,124 “Array-based microenvironment forcell culturing, cell monitoring and drug-target validation.”

Cellomics, Inc. U.S. Pat. No. 6,548,263 “Miniaturized cell array methodsand apparatus for cell-based screening.”

Fluidigm, Inc. Published Application 20040229349 (Nov. 18, 2004)“Microfluidic particle-analysis systems.”

Other References I

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SUMMARY

The present invention involves methods and systems related tomicrofluidic structures for sample preparation, culture, and/or forperforming assays or other clinical applications. Exemplary structuresprovided herein may be scaled to support cell cultures, cell-basedassays, molecular and cellular monitoring, monitoring, culturing andassaying using nano-beads or similar structures, and drug screeningprocesses. While a typical application of structures and methodsdescribed herein is in maintaining and/or growing cells in culture, theinvention can also be adapted to handle other objects on a cellularscale, such as coated and chemically or biologically active beads, etc.

In specific embodiments, the invention involves methods and systemsrelated to continuous cell-culture microfluidic systems. According tospecific embodiments of the invention, cells are cultured withcontinuous fluidic mass transport of medium and optionally with humidityand temperature control.

In further specific embodiments, the invention involves a high fluidicresistance ratio microfluidic device for culturing cells inside anarrangement (or array) of microchambers, providing a tool forcost-effective and automated cell or other culture.

In certain embodiments, materials used to fabricate cell culturecomponents are optically transparent, allowing one or more of variousmicroscopy techniques (e.g., phase contrast, fluorescence, confocal)without disturbing the culture environment. These properties enable therealization of a portable microfluidic cell culture array that can beused in sterile or non-sterile environments for research and commercialapplications.

In one example embodiment, a microchamber or a single unit of an arrayof culture areas consists of a roughly circular microfluidic chamber ofabout 40 to 50 μm in height with a high fluidic resistance fluidicpassage structure, such as passages of about 1 to 4 μm in height, thefluidic passage structure providing a fluidic connection to a mediumand/or reagent channel or area.

In another embodiment, the high fluidic resistance fluidic passagestructure comprises one or more of an (1) undercut connection of about 1to 4 μm, connecting to a medium channel, (2) a plurality of high fluidicresistance channels connecting between a culture area and a medium area;(3) a grid of high fluidic passages.

In another example embodiment, a microchamber or a single unit of thearray consists of a microfluidic chamber of about 40 to 50 μm with aflow-around medium/reagent channel connection to diffusion microconduits and with a single opening for receiving cells.

In further example embodiments, one or more micro culture areas areconnected to a medium or reagent channel via a grid of fluidic passages(or diffusion inlets or conduits), wherein the grid comprises aplurality of intersection micro high fluidic resistance passages. In oneexample, passages in the grid are about 1 to 4 μm in height, 25 to 50 μmin length and 5 to 10 μm in width, the grid allowing for more evendiffusion between medium or reagent channels and the culture area andallowing for easier manufacturing and more even diffusion.

According to specific embodiments of the invention, the high fluidicresistance ratio between the microchamber and the perfusion/diffusionpassages or grid (e.g., ratios in the range of about 10:1, 20:1 to 30:1)offers many advantages for cell culture such as: (1) size exclusion ofcells; (2) localization of cells inside a microchamber, (3) promoting auniform fluidic environment for cell growth; (4) ability to configurearrays of microchambers or culture areas; (4) ease of fabrication, and(5) manipulation of reagents without an extensive valve network. Theability to control the cell culture environment on the microscaleproduces many opportunities for improving biomedical andbiotechnological research.

In specific implementations, large turnover of the medium (e.g., about˜1/min) permits high cell density (e.g., >10⁷ cells/ml) and optionallythe use of CO₂ independent buffering of pH.

In specific embodiments, device fabrication is based on micromolding ofone or more elastomers (such as, polydimethylsiloxane (PDMS)), allowingfor inexpensive mass production of disposable multi-chamber or culturearea arrays. Other embodiments can be constructed from bondedsilicon/polysilicon surfaces or injection molded polymers.

In order to enhance control over the culture environment, the presentinvention in specific embodiments uses a two-level lithography process.This solves the issue of non-uniform mass transfer in microfluidicchannels caused by the parabolic laminar flow profile when directlyculturing cells inside the microfluidic channels. In other embodiments,a single-level lithography process is used, with the desired highfluidic resistance ratio achieved by construction diffusion passages ora diffusion grid with a small cross section, even if the passages havethe same height as the culture area.

The present invention, in further embodiments, involves an integrateddevice or system comprising cellular handling components, one or morecell culture arrays, fluidic connections and devices, and detection andor imaging devices. In specific example systems, the intersectionaldesign of cell culture chambers in an array provides independent cell orchamber addressing and/or allows varying of concentrations of substancesin culture medium, for example to provide for a large number ofdifferent cellular environments in a very compact cell culture chamberarray.

According to specific embodiments of the invention, aspects of theinvention can be incorporated into one or more integrated systems thatprovide simple yet elegant means for advanced cell culturing in acompact space providing an ideal mechanism for high throughputscreening, cells analysis, drug discovery, etc. In further specificembodiments, the novel methods and devices according to specificembodiments of the invention can be used in various systems.Applications include point of care diagnosis, tissue engineering,cell-based assays, etc.

While example systems according to specific embodiments of the presentinvention are described herein as used primarily for performing testingor characterizations of biological cells, it will be understood to thoseof skill in the art that a culture system according to specificembodiments of the present invention can be used in a variety ofapplications for manipulating and culturing devices at a roughlycellular size (4 μm-15 μm). These applications include, but are notlimited to: cellular systems, chemical systems, viral systems, proteinculturing, DNA culturing. In some such applications, known techniquesfor affixing substances of interest to micron or nano beads can be usedto facilitate such culturing.

In further embodiments, the invention can be integrated with a completeminiaturized cell culture system for high throughput cell-based assaysor other cell-based or bead based applications. A microfluidic cellculture array according to the invention offers an affordable platformfor a wide range of applications in high throughput cell-basedscreening, bioinformatics, synthetic biology, quantitative cell biology,and systems biology.

According to further specific embodiments of the invention, a portablecell culture array can be deployed in the field or clinic forpoint-of-care diagnostics of infectious agents or use in personalmedicine. For example, clinical cell culture is used for the detectionand identification of viruses, such as the causative agent of severeacute respiratory syndrome (SARS). Doctors can also derive importantinformation about individual patients from cultured biopsies, such asfor optimization of chemotherapy regimens.

The ability to perform inexpensive high throughput experiments usingmethods and devices of the invention also has applications in biologicalresearch, where thorough characterizations of experimental conditionsare currently limited. For example, configuration of a culture arrayaccording to specific embodiments of the invention allows the inventionto be loaded and handled using systems designed for conventional 96- or384-well microtiter plate and enables providing a different culturecondition in each chamber of an array according to specific embodimentsof the invention. In this example a cell culture device according tospecific embodiments of the invention can assay 96 or 384 differentconditions on a single chip.

In further embodiments, an array of the invention can be embodied in afully miniaturized system in a portable assay device, for examplethrough the integration of electro-osmotic pumps, optical sensors, andmicrophysiometers. A microfluidic cell culture array according tospecific embodiments of the invention can be involved with a wide rangeof applications in high throughput cell-based screening, bioinformatics,synthetic biology, quantitative cell biology, and systems biology.

Other Features & Benefits

The invention and various specific aspects and embodiments will bebetter understood with reference to drawings and detailed descriptionsprovided in this submission. For purposes of clarity, this discussionrefers to devices, methods, and concepts in terms of specific examples.However, the invention and aspects thereof may have applications to avariety of types of devices and systems. It is therefore intended thatthe invention not be limited except as provided in the attached claimsand equivalents.

Furthermore, it is well known in the art that systems and methods suchas described herein can include a variety of different components anddifferent functions in a modular fashion. Different embodiments of theinvention can include different mixtures of elements and functions andmay group various functions as parts of various elements. For purposesof clarity, the invention is described in terms of systems that includemany different innovative components and innovative combinations ofinnovative components and known components. No inference should be takento limit the invention to combinations containing all of the innovativecomponents listed in any illustrative embodiment in this specification.

In some of the drawings and detailed descriptions below, the presentinvention is described in terms of the important independent embodimentof a biologic array system and components thereof. This should not betaken to limit the invention, which, using the teachings providedherein, can be applied to a number of other situations. In some of thedrawings and detailed descriptions below, the present invention isdescribed in terms of a number of specific example embodiments includingspecific parameters related to dimensions of structures, pressures orvolumes of liquids, or electrical values. Except where so provided inthe attached claims, these parameters are provided as examples and donot limit the invention to other devices or systems with differentdimensions. All references, publications, patents, and patentapplications cited in this submission are hereby incorporated byreference in their entirety for all purposes.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A is an SEM picture of a early example single unit of a devicebefore bonding to a cover according to specific embodiments of theinvention showing four external ports: (1) perfusion/medium inlet, (2)perfusion/medium outlet, (3) loading, and (4) waste outlet and showingperfusion microchannels/passages that have a substantially lower heightor aspect than the other channels or the culture area.

FIG. 1B illustrates an SEM image of example perfusion/diffusion channeldimensions according to specific embodiments of the invention.

FIG. 2 is a photograph of an example 10×10 microfluidic cell culturearray or system bonded to a coverglass and mounted on a transparent ITOheater and shown connected to external fluid sources and positionedabove an imaging device according to specific embodiments of theinvention.

FIG. 3A-B illustrate a culture chamber array unit fabricated using softlithography techniques from a single mold and further illustrate achamber featuring an inner “C” barrier according to specific embodimentsof the invention.

FIG. 4A-C illustrate operation of a micro culture array device accordingto specific embodiments of the invention.

FIG. 5A-C illustrate operation of a micro culture array device accordingto specific embodiments of the invention showing long term patternmaintenance.

FIG. 6A illustrates a schematic view of a further example device orarray element with one cell loading port and a medium or reagent channelconnected thereto by a high fluidic resistance diffusion/mass transfermicro structure (eg micro inlets or passages) that have a substantiallyhigher fluidic resistance (due to lower height and/or smallercross-section) than the loading channel or culture area according tospecific embodiments of the invention.

FIG. 6B is a schematic block diagram showing four culture areas eachwith one loading port and a medium/reagent channel flowing proximate tothe culture areas and connected thereto by a high fluidic resistancediffusion/mass transfer micro structure according to specificembodiments of the invention.

FIG. 7 illustrates liquid mass transport through the example device,showing rapid convective transport through the outer channel (indicatedby the lighter colored fluid flow) with a slower diffusive transportacross the high fluidic resistance micro structure (indicated by theslow diffusion of the lighter colored fluid flow into the chamber areas)according to specific embodiments of the invention.

FIG. 8 illustrates a micrograph of example rat hepatocytes cultured inan example device such as in FIG. 6 wherein the fluorescence imagedepicts P450 metabolic activity of the same cells in a densely packedstate (A) and without cell contact (B) showing that a culture chamberaccording to specific embodiments of the invention is able to maintainpacked tissue cells in culture, allowing the cells to express morenormal metabolic activity.

FIG. 9A is a graph indicating viability of hepatocytes cultured on amicrotiter plate (▪), and in an example microfluidic culture deviceaccording to specific embodiments of the invention without cell contact(▴) and in a packed configuration in a microfluidic culture device (□),where the data represent mean and SEM of 139 culture units across 15independent chips and the graph indicates that viability of hepatocytesis greatly extended when cultured densely packed in a device of theinvention.

FIG. 9B shows P450 activity assayed by metabolism of5-chloromethylfluorescein diethyl ether (10 μM, 30 minutes) in amicrotiter plate (shaded) and in a microfluidic sinusoid of theinvention (hatched) showing significant improvement for primaryhepatocyte function (p<0.05) where the data represents mean and SD offluorescence intensity of >100 cells on 3 independent chips after 5 daysin culture (data normalized to microtiter plate hepatocytes).

FIG. 9C compares primary rat hepatoctye viability in a device of theinvention compared to a dish based culture method, indicating that in adish-based culture a biomolecular coating (e.g. collagen) is necessaryto keep cells alive, while in the microfluidic device, the uniqueculture chamber configuration is sufficient for cell viability over 7days without such coating.

FIG. 9D is a graph illustrating primary human hepatocytes cultured in adevice of the invention indicating that hepatocytes cultured accordingto the invention retain their liver metabolic activity.

FIG. 10A-C illustrates a micrograph of an example high densitymicrofluidic hepatocyte culture showing (A) time lapse (1 to 240seconds) images of hepatocytes loaded into the microfluidic sinusoidunder a driving pressure of 10 psi and (B) fluorescent viability assayon cells cultured for 7 days in the device at high cell density and (C)low cell density.

FIG. 11A is a micrograph of an example culture device with a grid-likeperfusion barrier according to specific embodiments of the invention. Inthis example, nanoscale beads (500 nm) are shown packed into the centralchamber to high density.

FIG. 11B is a close-up micrograph of an example of a culture device witha grid-like perfusion barrier according to specific embodiments of theinvention.

FIG. 12 is a series of micrographs illustrating an example device usedto culture human cancer cells into a high density tumor-like packedconfiguration over a 12 day period according to specific embodiments ofthe invention.

FIGS. 13 thru 18 are schematic block diagrams illustrating variousconfigurations for culture devices and/or systems according to variousspecific embodiments of the invention.

FIG. 13 illustrates as an example three out of possibly 100s of culturechambers in a system for multiplexed high cell density screeningaccording to specific embodiments of the invention.

FIG. 14 illustrates a variation with an addition of an in-line opticalor other detection region (represented with a red circle) according tospecific embodiments of the invention.

FIG. 15 illustrates as an example three out of possibly 100s of culturechambers in a system useful for drug penetration/absorption screeningwherein a solid mass of cells is cultured as described previously but incommunication with two separated fluid flows (left and right) accordingto specific embodiments of the invention.

FIG. 16 illustrates as an example one out of possibly 100s of culturechambers in a system wherein a first culture region is nested inside asecond culture region according to specific embodiments of theinvention.

FIG. 17 illustrates as an example three out of possibly 100s of mediumperfusion areas in a system useful in general purpose cell screeningaccording to specific embodiments of the invention.

FIG. 18 illustrates as an example three out of possibly 100s of culturechambers in a system useful where multiple culture areas are arranged inparallel with a single nutrient inlet and outlet (the multiple inletwells are connected off-chip) according to specific embodiments of theinvention

FIG. 19 illustrates a CAD drawing of a proposed 96-unit PMMAmicrofluidic bioreactor wherein in this example each well on thebioreactor is SBS standard size (3.5 mm in diameter) and the cellseeding columns are positioned in the center of the drug inlet andperfusate outlet wells; therefore, the bioreactor is compatible withstandard plate readers.

FIG. 20 shows the fabrication results of an 8-unit microfluidicbioreactor chip according to specific embodiments of the invention.

FIG. 21 illustrates (a) a prototype of pneumatic manifold for an 8-unitmicrofluidic bioreactor chip where priming of the chip and loading cellsinto the microfluidic structures can be accomplished through pneumaticpumping via the pneumatic control lines as illustrated and; (b) aninverted microscope used for monitoring during the process and showingsolenoid valves for controlling pneumatic pressure according to specificembodiments of the invention.

FIG. 22A through FIG. 22F illustrate a fabrication flow for an allplastic microfluidic plate using injection molding and adhesive bondingtechnology.

FIG. 23 illustrates a schematic fabrication process diagram for anexample fabrication according to alternative specific embodiments of theinvention.

FIG. 24 is a block diagram showing a representative example logic devicein which various aspects of the present invention may be embodied.

FIG. 25 (Table 1) illustrates an example of diseases, conditions, orstates that can evaluated or for which drugs or other therapies can betested according to specific embodiments of the present invention.

DESCRIPTION OF SPECIFIC EMBODIMENTS 1. Overview

The present invention in specific embodiments is directed to producing aminiaturized, inexpensive platform for “cell-culture-on-a-chip” to makehigh throughput cell experiments accessible in laboratory, clinical, andfield settings. Microfabrication and microfluidic technologies areadapted and extended according to specific embodiments of the invention.Microfabricated devices according to specific embodiments of theinvention can more precisely control cell culture environment than canmacroscopic systems.

In one example, microfluidic structures are implemented inside amicrofluidic device to provide large differences of fluidic resistancesof different microchannels. The device can therefore provide uniform andcontrollable microenvironment for continuous medium exchange cellculture. In another example, the microstructures are controlled bypressurized microchannels for flow regulation and for cellular samplepreparation. In yet another example, the high fluidic resistance (whichin some embodiments may be a result of a high aspect ratio fabrication)microstructures are positioned inside or adjacent to a microchamber ormicro culture area as a passive barrier for cellular and molecularsample immobilization. The device can further be integrated withelectrodes for functions such as metabolism monitoring, electro-chemicalproduct generation, electroporation, and a variety of otherapplications.

The design of a microscale cell culture device presents a number ofunique challenges, many of which have been recently discussed. Previousdemonstrations of cell culture on microfabricated devices include growthof hepatocytes, lung cells, and insect cells in both silicon and PDMSsubstrates. These works validated the biocompatibility, nutrient supply,and growth characteristics of cells within microfabricated devices, buthave yet to realize a high throughput array that can replicate the mainfunctionalities of traditional cell culture.

Primary cells (those removed from living humans and other animals)represent an important avenue of medical research due to their increasedrelevance to disease and healthy states. However, the limitedavailability of tissue donors and the technical difficulties ofmaintaining these cells in vitro have severely limited their applicationin biomedical research. Microfluidic systems according to variousembodiments of the invention can address these technical challenges byproviding an environment with microscale geometry/fluidic control thathas particular advantages for maintaining cell growth and/or cellviability and also in more closely creating the environment that certaintypes of cells would experience in their in vivo state, in particularthe densely packed or close proximity environment of living tissuesand/or solid tumors or other aggregations of cells. The inventionfurthermore enables such systems with low sample consumption, andautomated operation.

The present invention, according to various specific embodiments asdescribed herein, provides methods, systems, and devices that addressthe development of a novel high fluidic resistance and/or high aspectratio microfluidic cell culture array capable of providing a stable anduniform microenvironment for cell growth.

In specific embodiments, further elements such as heterogeneousintegration of a temperature control unit such as an ITO heater, allowthe invention to provide an automated cost-effective cell cultureplatform without the large robotic systems adapted by current practices.In specific embodiments, a microfluidic device of the inventionreplicates the major processes in traditional cell culture, making itadaptable to a large number of applications. As one example and fordiscussion purposes, 1×5 arrays are discussed for devicecharacterization to decrease the complexity of data processing and timeof optical monitoring. Other examples that are discussed herein and/orhave been fabricated include a 10×10 array, a 6×6 array, an 8×8 array,and an 8×1 array.

Example Device Configurations 2. Example 1 Example Experimental Chamber

FIG. 1A illustrates a top view of an example cell culture deviceaccording to specific embodiments of the invention. This example hasfour ports: perfusion inlet, perfusion outlet, reagent loading, andwaste, with the perfusion flow directed designated from left to right inthe figure and reagent loading from top to bottom in the figure. As canbe seen in the figure, the perfusion flow channels are separated fromthe main chamber by semi-circle-shaped perfusion channels at both theinlet (left) side and the outlet (right) side. Fluidic connectionbetween these semi-circle-shaped channels and the culture chamber ismade by the multiple high aspect ratio perfusion channels shown in thefigure, which are approximately 1/10 to 1/50 the depth of the mainchannels and/or culture chamber. To prevent cells from flushing awayduring perfusion, approximately 2 μm height perfusion channels connectthe perfusion inlets and outlets to the culture chamber. Because cells(typically >15 μm diameter) are inherently much larger than theperfusion channels (typically <15 μm diameter), most of the cells willstay inside the main culture chamber, which in this example is about 50μm in height and about 1 mm in diameter. The multiple small channelsused during perfusion also minimized shear flow over the cells andensured uniform medium distribution within the chamber. Additionally,since the narrow perfusion channels create a large fluid resistance,cell and reagent loading via those channels does not require the use ofmicrofluidic valves.

In specific embodiments, the microchambers are designed to have the samecell growth area as a typical well in a 1,536 well microtiter plate. Theleft and right ports are designed to provide continuous perfusion of themedium to the chamber for sustaining cell growth. The top and bottomports are used to load cells and reagents for cell-based assays.

In a more specific example implementation, each perfusion channel isabout 2 μm high and about 2 μm wide compared to the main culturechamber, which is about 1 mm in diameter and about 40 to 50 μm inheight. This high aspect ratio between the chamber and the perfusionpathway into it provides numerous advantages as discussed herein.

FIG. 1B illustrates an SEM image of example perfusion/diffusion channeldimensions according to specific embodiments of the invention. Thesescanning electron microscope pictures show aspects of a single unitdevice before bonding, with FIG. 1B showing a closer view of the highaspect ratio design, respectively. The perfusion channels serve two mainpurposes. First, since they are much smaller than the size of the cells(˜10 μm in diameter), they effectively prevent cells from being flushedaway or from migrating outside the chamber. Secondly, the multipleperfusion channels provide uniform nutrient access inside themicrochamber as will be discussed later.

It will be understood that numerous dimensional variations are possible,including chambers that are not circular, perfusion/diffusion channelsthat vary somewhat in dimensions between one and another, or otherdimensional parameters.

Arrays

In further embodiments, the invention can involve an array of cultureregions, such as the examples described above. FIG. 2 is a photograph ofan example 10×10 microfluidic cell culture array or system bonded to acoverglass and mounted on a transparent ITO heater and shown connectedto external fluid sources and positioned above an imaging deviceaccording to specific embodiments of the invention. A microfluidic cellculture system according to specific embodiments of the invention isdesigned to replicate the major processes applied in standard eukaryoticculture techniques. An example device is capable of providing a closedenvironment for cell growth and manipulation optionally without the needof an incubator. The bonded PDMS culture chambers maintain a sterileenvironment while permitting gas exchange with the atmosphere.Temperature can be controlled with a transparent ITO heater withouthindering monitoring of cells via optical microscopy. Humidity controlof the surrounding air can be used to prevent evaporation from themicrochannels, however, in specific embodiments, it has been observedthat the continuous perfusion of medium is sufficient to prevent thedevice from drying out. Stainless steel plugs with soft tubings can beconnected to the device and to a syringe pump for fluidic control. Cellgrowth can be using an optical microscope or other imaging device.

FIG. 2 can also include an optional microfluidic concentration gradientgenerator (such as discussed in Jeon et al. 2002) which is present inthe left top portion of the figure and that enables multiplexing cellbased assays under different conditions without increased samplepreparation time. Using only two inlet concentrations, a linear gradientis generated such that each column is exposed to a different reagentconcentration. Gradient generation across the columns of an example cellculture array according to these specific embodiments has beendemonstrated. Initial characterization of a ten channel splitterindicated that the flow was uniform within each column, and a differentreagent concentration can be introduced to different elements of thearray. There was no cross flow between columns due to the high fluidicresistance imposed by the perfusion/diffusion structures. Individuallyaddressing each column and row can furthermore be attained through theimplementation of a microfluidic valve network.¹⁵ By improving theefficiency of fluidic delivery, it is possible to introduce a level ofquantitative control to experiments that are traditionally qualitative.There is also great promise in adapting microfluidic cell culture forresearch in tissue engineering.¹⁶

3. Example 2

A further example nanoliter scale fluidically addressable microfluidicplatform according to specific embodiments of the invention is describedbelow. In a specific example, an addressable 6×6 array of eightnanoliter chambers is effective for long term continuous culture of theHeLa human cancer cell line with a functional assay of 36 differentcellular microenvironments. In one optional construction, high aspectratio soft lithography is used to create the high fluidic flow channels,though further study has shown that the same high fluidic resistance canbe achieved using a diffusion structures with diffusion passages thathave the same height a the main chamber and medium channels. In thisexample, a “C” shaped ring with a narrow gap along the base is used tofurther separate individual culture units from flow channels toeffectively decouple cell growth regions from pressure-driven transportwithout the use of active valves. This design avoids problemsencountered in some multiplexing nanoliter culture environments byenabling uniform cell loading, maintaining long term cell localization,eliminating shear and pressure stresses on cultured cells, providingstable control of fluidic addressing, and permitting on-chip opticalmonitoring. The device uses a novel microstructure consisting of a highfluidic resistance roughly “C” shaped cell localization ring, and a lowresistance outer flow ring. The central growth area and flow ring in oneexample were fabricated to be 50 μm in height, allowing cell transportthrough the device. The “C” shaped cell localization ring defining the 8nl cell growth area consisted of a barrier with a 2 μm opening along thebase with an inner diameter of 450 μm. This space allowed fluid flowthrough the cell growth area, but was narrow enough to retain cells inthe central ring. An example single unit of this structure isillustrated in the SEM photograph shown in FIG. 3A.

FIG. 3A-B illustrate a culture chamber array unit fabricated using softlithography techniques from a single mold and further illustrate achamber featuring an inner “C” barrier according to specific embodimentsof the invention. In this example, the device material consisted of PDMSelastomer covalently bonded to a tissue culture grade coverglass. FIG.3B is an SEM image of an example single unit of an array according tospecific embodiments of the invention. A central growth area was definedwith a 450 μm diameter “C”-shaped localization ring with wallsfabricated with a 2 μm opening along the bottom that retained cellswhile permitting nutrient and fluid transport (cross section A-A′).Cells were loaded into the central chamber through the opening at themouth of the “C”-shape. The scale bar represents 100 microns. Thisdesign allows high density arrays without the need for alignment. Thelower portion of FIG. 3B illustrates schematically a cross section ofthe device shown in the upper portion of FIG. 3B.

In these embodiments, the individual array unit consisted of a highfluidic resistance inner chamber for cell growth and a low fluidicresistance outer channel for fluid flow. The 10³-fold difference inresistance between the two compartments allows uniform loading of thearray, controlling cell concentration, and maintaining long-term patternintegrity by selective removal of cells outside the growth area.

In an example device, these capabilities are integrated with aspects ofthe microfluidic cell culture array described above to produce a 6×6addressable cell microarray for long-term functional studies. A singlemold process with no required surface treatment used for fabricationallows the array to be easily scaled to a much higher size and density.In one example, a 6×6 cell analysis array with four fluidic paths toeach chamber was achieved by fabricating an 8×8 matrix and sacrificingthe outer row and column of culture units due to slight flownon-uniformities near the edges.

According to specific embodiments of the invention, the inlet and and/orexit of each column or row can comprise different microfluidic interfacedesigns, for example: (1) a multiplexer (a single connection formultiple rows), (2) a concentration gradient generator, or (3)individually addressable connections. The gradient generator was amodified version of published work, and served to create multiplereagent concentrations from two fluidic inlets.

In alternative embodiments, the perfusion ring can be replaced to a highresistance passage into the outer ring, as illustrated in FIG. 3B. Infurther embodiments, the basic configuration as shown in FIG. 3A-B canbe used for single-cell culture and trapping, which is useful in variousapplication as will be understood in the art. In some embodiments, thecell chamber size can be reduced for optional single-cell trappingoperation.

Example Operation

The 6×6 prototype is capable of culture and assay of 36 differentcellular microenvironment conditions. In proof of concept experiments,human cancer cells (HeLa) were loaded into the array and cultured for 7days to approximately 5*10⁷ cells/ml with a viability of over 97%. Rowand column addressing was demonstrated by integrating a microfluidicconcentration gradient generator to both dimensions, providing adifferent assay condition for each array unit using only 4 inletreagents. Alternatively, individually addressing of each row can be usedto allow many different reagents, drug exposure times, or time points tobe assayed in this dimension.

After suspended HeLa cells were loaded into the array until the desiredconcentration was obtained, fresh culture medium was introduced to flushresidual cells from the microfluidic channels. After loading, cells werecultured to obtain a high cell density (˜300 cells/chamber). Selectivemaintenance was conducted every 24 hours to ensure pattern integrity.Array capabilities were demonstrated.

A finite element model was created to predict the fluid velocity profilethrough this structure. This analysis indicated a 10³-fold difference influid resistance between flow through the inner chamber and outerchannel, agreeing with the analytical approximation based onHagen-Poiseuille flow. This prediction was verified by tracking the flowof 2 μm beads through the microfluidic device.

Cell Loading

In this example, cell loading rate was controlled using a programmablesyringe pump. For observation of cell flow through the microfluidicarray, a flow rate of 40 nl/min/column was used, resulting in a flowthrough of approximately 0.7 cells/sec/unit. In a 100 second period, 218cells were observed to flow through 3 separate loading columns,verifying the predicted flow rate. Cell flow velocity data within thedevice was obtained from analysis of time lapse digital recordings from131 cells for the outer channel and 53 cells for the inner growth area.Uniformity of cell loading was quantified by counting cell numbers ineach unit of the 6×6 array after a 2 minute loading period at 500nl/min/column. The control condition was loaded in a 6×6 array withoutcell localization structures. Loading uniformity was calculated as themean±SD (standard deviation) of the final number of cells in each row ofthe array, with row 1 being the closest to the inlet channel.

FIG. 4A-C illustrate operation of a micro culture array device accordingto specific embodiments of the invention. Due to the high fluidicresistance of flow through the 2 μm localization ring, the bulk ofconvective transport passed through the outer channel. This designlargely decoupled the effects of pressure driven flow on cultured cells.In FIG. 4A, HeLa cell suspension was flowed through the unit at 40nl/min to load the central rings. The cell indicated by the blue arrowwas loaded into the chamber, while the cell specified by the red arrowflowed through the outer channel. In FIG. 4B, after 1 second, thedifference in flow resistance was evident based on tracking the two cellvelocities. In FIG. 4C, the microfluidic structure served as a cellconcentrator, allowing a high density of cells to be seeded into eachchamber. Since the fluidic pressure and shear stress exerted on thecells within the central ring was negligible, high cell viabilities wereobserved.

With a cell loading rate of 40 nl/min through each chamber, cellvelocities were observed at 440±80 μm/s in the flow channel and 0.8±0.3μm/s in the culture chamber, giving a velocity ratio of 550. Thisindicated that the flow rate through the central area was in the rangeof 50 pl/min. Under these conditions, the time scale of small moleculediffusion through the growth area (1.7 minutes) was over 4-fold fasterthan convective transport. The diffusion dominated mass transfereliminated shear stresses caused by traditional continuous flowtechniques while maintaining a microenvironment amenable for tissuegrowth. The continuous diffusion of chemicals into the cultureenvironment may also provide a more physiologically accurate model forin vivo reaction kinetics. Additionally, the slow time scale forcellular exposure to reagents can dampen out fluctuations in assayconditions for long term studies.

The uniformity of cell loading in the 6×6 array (19% standard deviationwith a minimum of 47 cells) was significantly improved compared to amicrofluidic array without the loading structures under the sameconditions (150% deviation with 47% of chambers empty). Initial analysisindicated that roughly 1-5% of cells entered the growth chamber. Thiswas significantly larger than the predicted 0.2% of total flow, duelargely to the tendency of cell clusters to preferentially enter thelocalization ring. The 2 μm opening under the cell localization ringalso served as a cell concentrator by preventing trapped cells fromleaving the chamber. By varying the loading flow rate and time, it waspossible to completely fill the culture chambers with cells (˜5*10₇cells/ml). Once the cells were localized in the central growth area,they became essentially decoupled from pressure fluctuations in theattached tubing, ensuring that the cells will attach and grow in thedesired regions.

Cell Culture

All microfabricated components were sterilized with UV light prior touse. Fluidic connections were sterilized with 70% ethanol and thoroughlyrinsed with filtered deionized water prior to use. The device wascapable of maintaining a sterile environment while being continuouslyhandled in a non-sterile manner because all fluidic connections weresealed with epoxy, isolating the microfluidic device from the outerenvironment.

Cells were cultured with continuous perfusion of CO₂ Independent Medium(Gibco, Inc.) supplemented with 10% fetal bovine serum, 4 mML-glutamine, and 1% penicillin/streptomycin. During perfusion, thedevice was placed inside a 37° C. incubator. Perfusion was controlledwith a programmable syringe pump (Cole Parmer 74900), typically set at0.4 μl/min flow through the arrayed device. Cells were cultured for overtwo weeks within the microfluidic array with no loss of viability.

Pattern Maintenance

As the cells began to divide within the array, it was possible tomaintain the localization pattern by selectively removing cells fromoutside the growth area. The protease trypsin was introduced to thearray to release the adherent cells from the substrate. The large flowvelocity in the outer channels caused these cells to be removed from thesystem while cells in the growth rings were retained. Replacing culturemedium to the chambers caused these cells to reattach to the substrateand resume growth. By periodically repeating this process, the cellmicroarray pattern could be maintained for long periods. In thisexperiment, the cells were purposefully allowed to overgrow the chambersto demonstrate the limits of pattern maintenance. Even when the cellshad completely overgrown the outer channel, selective removal wascapable of restoring the pattern such that less than 3% of cellsremained outside the central ring. Scheduling treatment every 24 hoursensured over 99% of all cells remained within the central ring. Morestringent control of reaction conditions and scheduling can largelyeliminate residual cell debris in the outer channel. The ability tomaintain cellular localization is crucial for microscale arraydevelopment by preventing flow non-uniformities resulting from cellgrowth into the fluidic channels.

FIG. 5A-C illustrate operation of a micro culture array device accordingto specific embodiments of the invention showing long term patternmaintenance. In FIG. 5A, after extended culture, dividing cells began tooccupy the fluidic channels. In FIG. 5B, using the trypsin protease,cells were suspended from the substrate and selectively flushed from theouter channel. Since the flow velocity was orders of magnitude lower inthe central chamber, these cells were not displaced, and continuedgrowth once medium was restored to the device. In FIG. 5C it is shownthat this method ensured long term cellular localization (closedcircles) compared to a control condition where no selective removal wasimplemented (open circles). Pattern degradation was defined as thepercent of cells growing outside the central chamber.

Real-time analysis of cellular activity was readily achieved usingoptical interrogation. The transparency of the microfabricated device atbiologically relevant wavelengths permitted seamless adaptation tofluorescent microscopy techniques used in cell biology. Single cellanalysis using Raman spectroscopy on bio-functionalized nanoparticleswithin the cell culture microarray can also be used to monitor activity.The culture units could also be linked to downstream microfluidicanalysis modules, such as one developed for single cell nucleic acidisolation and detection.

4. Example 3

In a further embodiment, a culture chamber has a single opening for cellintroduction and a diffusion culture medium or reagents channel thatflows around the culture chamber and is connected thereto by microinlets or micro perfusion channels. FIG. 6A illustrates a schematic viewof a further example device or array element with one cell loading portand a medium or reagent channel connected thereto by a high fluidicresistance diffusion/mass transfer micro structure (eg micro inlets orpassages) that have a substantially higher fluidic resistance (due tolower height and/or smaller cross-section) than the loading channel orculture area according to specific embodiments of the invention. As withother embodiments described herein, the high fluidic resistance betweenthe passages and the microchamber allows for easy cell handling andculture. This example embodiments has particular applications forcreating and/or maintaining an improved artificial tissue unit, such asan artificial liver, pancreas, kidney, thyroid, etc., for various assaysand also as an improved solid tumor model.

FIG. 6B is a schematic block diagram showing four culture areas eachwith one loading port and a medium/reagent channel flowing proximate tothe culture areas and connected thereto by a high fluidic resistancediffusion/mass transfer micro structure according to specificembodiments of the invention. This should be understood as one basicexample embodiment. In alternative embodiments, the culture chambers canhave different geometries, such as the “U” shaped chamber illustratedbelow. One aspect of this embodiment is that the medium/culture channelflows around the microchamber without being forced to flow through themicrochamber as illustrated in some alternative perfusion embodimentsdescribed above. Thus, transfer of nutrients, wastes, or reagents inthis embodiment is largely by diffusion. However, as discussed above,even in perfusion embodiments, some portion of the mass transfer is dueto diffusion. In other embodiments, all chambers or several sets ofchambers can have a shared cell loading channel as shown, but separatedmedium channels, allowing for a number of individual experiments to beperformed on multiple duplicate cultures.

While this example embodiment has a number of applications, one ofparticular interest is use in facilitating an artificial liver orartificial liver sinusoid. In an example implementation, high densityprimary rat hepatocytes received nutrient transport via a biomimeticmembrane (or vasculature or virtual membrane) according to specificembodiments of the invention. This configuration demonstrated enhancedviability and cytochrome P450 metabolic activity compared to cultureslacking this multicellular architecture.

The ability to maintain liver specific function of hepatocytes in vitrois an important area of medical and pharmaceutical research due to theircentral role in drug metabolism. As with most tissues, hepatocytesrapidly lose organ specific function once they are removed from the invivo environment. While extracellular matrix coatings such as collagen Iare traditionally used to maintain primary hepatocytes in culture, thisis also known to down-regulate liver specific activity By utilizingengineering capabilities with micron-scale resolution, the presentinvention makes it possible to recreate portions of a natural liverarchitecture.

In one example, a microfluidic artificial sinusoid was fabricated usingsoft lithography methods as described herein, and consisted ofstructures molded in silicone elastomer bonded to a glass culturesurface. An example basic culture unit contained a 50×30×500 μm hepaticplate, a 50×30 μm cross section vessel, and a biomimetic “endothelialbarrier” (or virtual membrane) separating the hepatocyte culture regionfrom the nutrient transport vessel, wherein this biomimetic barrier orvirtual membrane is constructed from one or more high fluidic resistancepassages using fabrication as described herein.

The microfluidic culture unit mimics properties of liver vasculature inliving tissue. Hepatocytes are prepared as a nearly solid mass of cellsin “plates” about 50 μm in width. On either side of the hepatocytes arenutrient transport “sinusoids.” Small cross section channels connectingthe two compartments localize cells in the growth areas while allowingdiffusion of medium. The flow rate (˜5 nl/min), fluid velocity (˜0.5-1.5mm/sec), and cell number (˜250-500) approximate values found in theliver. The high fluidic resistance ratio design between the cell seedingcolumns and the medium channels allow diffusion-dominant mass transferfor tissue culture. The small medium channels also prevent hepatocytesfrom growing into the nutrient supply channels. Thus, in particularembodiments, the present invention functionally recreates themicro-environment found in the normal human liver. In a normal liver, a“hepatocyte plate” is what physiologists typically call the aggregationof hepatocytes located between sinusoid spaces (empty regions allowingfor blood flow). This configuration maximizes the number of functionalcells without restricting nutrient transport. In many organs,endothelium-lined sinusoids (or spaces) provide the micro-environmentfor the cells that make up the tissues of an organ and tissues fromthese organs, as well as other tissues, are particularly suited toculturing as described herein.

Returning to the example embodiment shown in FIG. 6, narrow pores withinthe “endothelial barrier” (e.g., about 1 to 2 μm wide by×1 to 2 μm up tothe height of the culture area tall) prevented cells from passingthrough, but permitted diffusive transport of wastes and nutrients. Ananalysis of the fluid dynamics of this microfluidic architectureindicated that the rate of nutrient diffusion into the hepatocyteculture region was roughly 100-fold greater than convective transport atthe physiologically relevant blood flow rate of 10 nl/min. Furthermore,the artificial endothelium was also used as a cellular sieve toconcentrate hepatocytes from suspension up to 10⁴-fold (e.g., as shownin FIG. 8 and FIG. 10) in order to create a compacted hepatocyte platein vivo.

In order to compare the function of the artificial sinusoids accordingto specific embodiments of the invention to other liver cell culturetechniques, isolated rat hepatocytes (Cambrex) were maintained in thesuggested medium on 384-well glass bottom plates and microfluidicsinusoids at two initial cell densities. In the absence of collagencoating, hepatocytes in the microtiter plate and those lacking densecell-cell contacts lost viability within 4 days. Plating hepatocytes atan equivalent density (2×10⁵ cells/cm²) in the microtiter plate did notimprove viability. An assay of liver specific P450 activity verified theincreased functionality of the hepatocytes cultured in the microfluidicsinusoid (FIG. 9B). Metabolic activity was statistically equivalent fromday 1 to day 7 in the microfluidic device (p>0.20). FIG. 8 illustrates amicrograph of example rat hepatocytes cultured in an example device suchas in FIG. 6 wherein the fluorescence image depicts P450 metabolicactivity of the same cells in a densely packed state (A) and withoutcell contact (B) showing that a culture chamber according to specificembodiments of the invention is able to maintain packed tissue cells inculture, allowing the cells to express more normal metabolic activity.

FIG. 9A is a graph indicating viability of hepatocytes cultured on amicrotiter plate (▪), and in an example microfluidic culture deviceaccording to specific embodiments of the invention without cell contact(▴) and in a packed configuration in a microfluidic culture device (□),where the data represent mean and SEM of 139 culture units across 15independent chips and the graph indicates that viability of hepatocytesis greatly extended when cultured densely packed in a device of theinvention. FIG. 9B shows P450 activity assayed by metabolism of5-chloromethylfluorescein diethyl ether (10 μM, 30 minutes) in amicrotiter plate (shaded) and in a microfluidic sinusoid of theinvention (hatched) showing significant improvement for primaryhepatocyte function (p<0.05) where the data represents mean and SD offluorescence intensity of >100 cells on 3 independent chips after 5 daysin culture (data normalized to microtiter plate hepatocytes).

These findings indicate that the close physical contact of hepatocytesin the microfluidic sinusoid influences differentiated function. Thisconclusion agrees with findings on hepatocyte aggregate behavior and maybe due to the importance of functional gap junctions in the intact liver(e.g., in S. A. Stoehr, H. C. Isom, Hepatology 38, 1125 (November,2003). Microfluidic engineering enables the control of key aspects ofmulticellular architecture while at the same time solving the problem ofproviding adequate mass transfer into tissue density cultures. Theapplication of engineering principles described here can prove usefulfor the future investigation of organ function.

FIG. 10A-C illustrates a micrograph of an example high densitymicrofluidic hepatocyte culture showing (A) time lapse (1 to 240seconds) images of hepatocytes loaded into the microfluidic sinusoidunder a driving pressure of 10 psi and (B) fluorescent viability assayon cells cultured for 7 days in the device at high cell density and (C)low cell density. The loading process is self-limiting since theresistance to flow through the sinusoid increases with cell density.Note the close cell packing attained with minimal membrane stress. Inthese experiments, cells were stained with Hoechst 33342 (blue), calceinAM (green), and ethidium homodimer-1 (red). Low cell density was definedas a mean center-to-center spacing of >23 μm and high density defined as<20 μm. The mean hepatocyte diameter was 20±2 μm.

5. Example 4 Grid Barrier

An alternative embodiment to any of the devices discussed hereininvolves a grid-like diffusion or perfusion barrier between themedium/reagent channel and the culture area. This barrier can beconstructed in a similar way to the micro inlets or passages asdescribed above, except instead of individual inlets, a grid or otherarrangement of intersecting micro inlets is used to allow perfusionfluid transport. FIG. 11A is a micrograph of an example culture devicewith a grid-like perfusion barrier according to specific embodiments ofthe invention. In this example, nanoscale beads (500 nm) are shownpacked into the central chamber to high density. As with the micropassages described above, the grid passages can be much shorter than theculture area or can be near to or at the same height, according tospecific embodiments of the invention.

6. Example 5 Multicellular Tumor Spheroid Model

Another application of the invention is to culture solid tumors that canperform a similar function as multicellular tumor spheroid models forcancer drug screening. Multicellular tumor spheroids (MTS) are denselypacked cancer cells grown generally in suspension in culture that mimicproperties of tumors inside a living organism. While MTS's are known toprovide a better model for cancer drug efficacy than plate culturedtumor cells, they are limited in practice due to the difficulty ofspheroid handling and difficulty in observing suspended spheriods. Usingthe microfluidic method described here, a much improved method toproduce high density tumor-like cultures in defined structures isachieved.

Thus, according to specific embodiments of the invention, afterprolonged culture of cancer cells in a microfluidic culture chamber, thecells undergo a transition in morphology and assume behavior like thatfound in MTS. In this condition, extensive cell-cell contacts are madethat limit drug penetration into the cell mass, an extracellular matrixis produced, and individual cell boundaries become obscured. FIG. 12 isa series of micrographs illustrating an example device used to culturehuman cancer cells into a high density tumor-like packed configurationover a 12 day period according to specific embodiments of the invention.

7. Other Examples

FIGS. 13 thru 18 are schematic block diagrams illustrating variousconfigurations for culture devices and/or systems according to variousspecific embodiments of the invention. While several diagrams primarilyillustrates as the array element a squared ‘U” culture chamber, it willbe understood that any of the other culture chamber configurations asdiscussed herein could be configured as illustrated below according tosome embodiments of the invention. In a number of these figures, thefluidic connections to each culture chamber are shown as separate.However, in various embodiments, these connections can be combinedeither on-chip or off-chip to provide larger effective culture areas orfor ease of maintaining nutrient flow or collecting chamber output.

FIG. 13 illustrates as an example three out of possibly 100s of culturechambers in a system for multiplexed high cell density screeningaccording to specific embodiments of the invention. In this example,cell samples are concentrated into tissue-like regions as defined by themicrofluidic barriers and maintained with a continuous flow of reagentson both sides of the cell sample. This design can be used to mimictissues such as the liver sinusoid. This is particularly well suited forstudies that involve the culture of tissue-like samples (e.g. primarycell samples). Using a single cell inlet port, multiple cell chamberscan be filled, where each can then be treated with a differentdrug/medium combination. Cell behavior can be analyzed via microcopymethods or by collecting the flow through and performing biochemicalanalysis.

FIG. 14 illustrates a variation with an addition of an in-line opticalor other detection region (represented with a red circle) For many cellbased assays, endpoints are measured from the fluorescence intensity ofsoluble probe substrates. In this design, a microscope or spectrometeris focused on the downstream detection region to quantify cellularactivity. This configuration is especially attractive for a microfluidicplatform since the fluid volumes utilized are typically minimal (1-1000nL), making traditional “bulk” measurement difficult.

FIG. 15 illustrates as an example three out of possibly 100s of culturechambers in a system useful for drug penetration/absorption screeningwherein a solid mass of cells is cultured as described previously but incommunication with two separated fluid flows (left and right) accordingto specific embodiments of the invention. In this example, a solid massof cells is cultured as described previously, and in communication withtwo sets of fluid flows (e.g., left and right). In this configuration, achemical of interest can be introduced into one flow channel (e.g., adrug), and monitoring of the presence of the chemical or some by productor metabolite or result thereof in the opposite channel enables thedetermination of drug transport kinetics and/or drug activity. This typeof experiment is useful for calculating the extent of drug penetrationor absorption through a tissue like culture. For example, many cancerdrugs are rendered ineffective due to their inability to penetrate intothe center of solid tumors. Another example is the need forpharmacologists to determine how much of a drug compound (present in theblood or digestive system) will absorb into body tissues such as bloodvessels and intestinal linings. This microfluidic design uniquelyenables the high throughput screening for these activities.

FIG. 16 illustrates as an example one out of possibly 100s of culturechambers in a system wherein a first culture region is nested inside asecond culture region according to specific embodiments of theinvention. In this example, one cell culture region is nested inside asecond culture region. This allows the loading of two different celltypes into defined locations in communication with each other. Oneapplication of this design is for the generation of an artificialmulti-layer tissue such as a hepatocyte/endothelial structure. Theability to culture multiple cell types in contact with each other isknown to improve physiological behaviors. In further embodiments, thefabrication techniques as described herein can be used to createstructures of more than two cellular culture areas.

FIG. 17 illustrates as an example three out of possibly 100s of mediumperfusion areas in a system useful in general purpose cell screeningaccording to specific embodiments of the invention. This configurationmay be desirable for use in general purpose cell screening. This deviceconfiguration does not concentrate the cells into a solid mass. Instead,similar to a conventional microtiter plate, the cells are distributedrandomly along the culture channel. A high resistance microfluidicbarrier separates the cell culture chamber from a parallelnutrient/reagent channel. This configuration replicates many of theproperties of conventional macro-scale cell screening, with theadvantage of a microfluidic format. One key application for this designis for performing high throughput primary cell experiments, which can beprohibitively expensive due to the large quantity of cells required perdata point.

FIG. 18 illustrates as an example three out of possibly 100s of culturechambers in a system useful where multiple culture areas are arranged inparallel with a single nutrient inlet and outlet (the multiple inletwells are connected off-chip) according to specific embodiments of theinvention. As one example application, this configuration mimics humanliver organ tissue when hepatocytes are used. This manner ofmultiplexing allows many microscale units to be maintained, generatingan artificial organ environment. One application of such a design wouldbe to create an artificial liver for use in preclinical drug screening(drug metabolism and pharmacokinetics). Another potential application isfor construction of an artificial organ to produce a compound orsubstance of interest or to perform a biologic or therapeutic function.In this example design, each well on the bioreactor is SBS standard size(3.5 mm in diameter) and the cell seeding columns are positioned in thecenter of the drug inlet and perfusate outlet wells; therefore, thebioreactor is compatible with standard plate readers.

Primary Cell Applications

In addition to the described experiments, a chamber array according tothe invention is suited for use with all currently utilized primary cellsamples. Primary cells are those harvested from living animal tissue,and are particularly useful for tests where physiological responses areimportant (e.g. drug screening). Companies such as Cambrex and AllCellsare specialized in preparing and selling primary cell samples. Due tothe limited supply of primary cell samples, they are not easilyintegrated into large scale screens. The advantage of a controlledmicrofluidic format is that with the same number of cells, thethroughput of experiments can be increased by 100×. Additionally, sinceit is important to maintain primary cell function in culture, amicrofluidic system enables better control of culture conditions.

A special category of primary cells are stem cells. These cells arecapable of differentiation into various cell phenotypes under differentconditions. For example, the human embryonic stem cell is known to beable to differentiate into every cell type found in the adult humanbody. Stem cell culture currently is practiced by maintaining highdensity colonies of stem cells in well controlled environments.Therefore, the invention described here is ideally suited forapplications in stem cell culture, maintenance, and controlleddifferentiation.

System Example

In one example embodiment, operation of the artificial livermicrofluidic device is accomplished using an interface platform witheach example chip containing 8 independent cell culture experiments,with a separate inlet and outlet reservoir. FIG. 20 shows thefabrication results of an 8-unit microfluidic bioreactor chip accordingto specific embodiments of the invention. A novel fabrication processwas developed to sandwich PDMS microfluidic structures between PMMA andglass. The PMMA/PDMS composite chip was then bonded to a PMMA well plateusing acrylic adhesives. The operation of the bioreactor chip wasverified by confirming food dyes flowing from the top reservoirs to thebottom reservoirs through the PDMS microfluidic structures. In thisexample, the culture microchambers and microfluidic connections arelocated on a central area, interfaced to an SBS standard well format(e.g., a standard size for 384 well plates). In the figure, blue and reddyes are shown at alternating inlet reservoirs at one side of the chip,with the outlet reservoirs at the other side of the chip. This exampleconfiguration allows eight independent cell culture experiments, witheach of the eight separate regions in the central portion having one ormore sinusoid microchambers as described herein. At right in the figureis pictured an optional manifold used for flow control in this example.However, gravity flow can also be utilized as described herein. The chipis inserted into the manifold, which provides precise pneumatic pressurecontrol for medium/reagent flow. The transparent chip and manifold isdepicted on a microscope stage, where cell behavior can be readilymonitored.

Thus, this embodiment provides independent addressable medium/reagentchannels that are not connected. For example, in one configuration asshown in FIG. 20, each inlet port/reservoir connects to exactly oneoutlet, allowing, for example, testing of 8 different chemicals byplacing 8 separate liquids into the 8 inlet ports. While in thisexample, each of the 8 units shares the same cell loading inlet, due tothe high resistance barrier in each unit, there is functionally nocommunication between the 8 “independent” inlet/outlet flows.

In an example operation, cell loading is performed on all eight chamberssimultaneously, allowing significant cell savings. Thepoly-dimethyl-siloxane (PDMS) based microfluidic device is interfacedwith a standardized “well plate” format (acrylic), allowing directpipetting of culture medium and reagents. The fabrication of the chipenables visualization of all fluidic flows using standard microscopy orhigh content screening methods. For cell loading and initial priming, acustom built air pressure control manifold is used. Due to the low flowrates necessary for medium perfusion (˜5 nl/min), a simple gravitydriven flow method by tilting the plate to make inlet wells higher thanthe outlet wells in conjunction with fluidic resistance patterningmethod can be used to achieve reliable operation in some embodiments,though other pumping mechanisms can also be used.

The microscale nature of the culture device enables research to beperformed with significant cell/reagent savings. In current operation,it takes only 5,000 cells (5 μl at 10⁶ cells/ml) to completely fill the8 unit device. Currently, cell loading is accomplished in under 5minutes with over 90% of the cells localized to the growth regions.Further optimization is expected to increase the loading efficiency tonearly 100% (all cells placed in the well end up in the microfluidicgrowth region) by standardizing the cell loading conditions (celldensity, loading medium, flow rate) to minimize cell loss in theupstream fluidics. In preliminary observations, a medium flow rate of 5nl/min (˜8 μl/day) was sufficient to maintain HepG2 cells. Therefore,the standard 384 microtiter well size inlet and outlet reservoirs(containing 100 μl) are sufficient to maintain long term culture (withoccasional replenishment). Flow rate through the device during cultureis maintained using gravity driven hydrostatic pressure. This isachieved by placing the chip on a fixed incline. By carefully designingthe fluidic resistance in the microfluidic channels and the inclineangle, initial observations show that a 7.4±1.1 nl/min can be sustainedover long periods. The tolerance of this flow (15%) is expected to bemuch better (<2%) by improving the quality and uniformity offabrication.

Cell culture within the array was verified using the HepG2 humanhepatoma cell line. These observations indicate that there is nonutrient limitation even for very high density cultures after 7 days ofgravity driven flow. Furthermore, the viability remained nearly 100% inall 8 units on the chip, and across 3 independent chips, indicating thatthere are no fundamental flaws in the design or operation.

Preliminary observations of primary rat hepatocyte (Cambrex Bioscience)culture in the device indicated a similar altered morphology that is notobserved in plastic dish culture (FIG. 8). Presumably, the cell-cellcontact enabled by the microfluidic device signals the formation of“liver-like” aggregates, similar to those observed in ECM and spheroidculture. Preliminary data indicates that this culture configurationgreatly enhanced cell viability (FIG. 9). Even in the absence of surfacecoating, cell-cell contact seemed capable of maintaining high hepatocyteviability in the microfluidic format.

FIG. 21 illustrates (a) a prototype of pneumatic manifold for an 8-unitmicrofluidic bioreactor chip where priming of the chip and loading cellsinto the microfluidic structures can be accomplished through pneumaticpumping via the pneumatic control lines as illustrated and; (b) aninverted microscope used for monitoring during the process and showingsolenoid valves for controlling pneumatic pressure according to specificembodiments of the invention. As described herein, in specificembodiments a novel fabrication process was developed to sandwich PDMSmicrofluidic structures between PMMA and glass. The PMMA/PDMS compositechip was then bonded to a PMMA well plate using acrylic adhesives. Theoperation of the bioreactor chip was verified by confirming food dyesflowing from the top reservoirs to the bottom reservoirs through thePDMS microfluidic structures. In an example setup, after chips wereloaded, they were put into a CO₂ incubator (Ferma Scientific) forenvironment control. An inclined design gravity flow rack is used forlarge scale perfusion experiments. The flow rate resolution is atnanoliters.

8. Example Fabrication Methods

Systems and devices as described herein can be fabricated using anytechniques or methods familiar from the field of photolithography,nano-fabrication, or micro-fluidic fabrication. For completeness of thisdisclosure and to discuss additional and independent novel aspectsaccording to specific embodiments of the invention, specifics of examplefabrication methods are provided below.

In some embodiments, the microdevices are fabricated using a single moldprocess, allowing direct array scale-up as well as the capability ofintegration with additional microfluidic layers. The development of amicrofluidic high throughput automated cell-based assay platform allowsrapidly determining or observing multiple cellular parameters forapplications in quantitative cell biology and systems biology.

In alternative specific embodiments, a high density, scalablemicrofluidic cell array is implemented using a novel design tomechanically decouple cellular compartments from fluid flow. This isaccomplished again using a method of high aspect ratio soft lithographytechnology, which consists of patterning two different channel heightsand/or two different channel widths on a single mold such that fluidicresistance can be finely controlled over up to five orders of magnitude.By localizing cell growth to predefined areas, fluid transport throughthe array is carefully controlled and isolated from cellular activity.

FIG. 22A through FIG. 22F illustrate a fabrication flow for an allplastic microfluidic plate using injection molding and adhesive bondingtechnology.

FIG. 23 illustrates a schematic fabrication process diagram for anexample fabrication according to alternative specific embodiments of theinvention. An example microfluidic cell culture array according tospecific embodiments of the invention was fabricated by usingsoft-lithography technology and replicate molding. This processconsisted of patterning a polymer mold on a silicon wafer followed byreplication with a soft elastomer. SU-8 negative photoresist (MicrochemCorportion) was used as the mold material. First, the SU-8 2002 waspatterned on a silicon wafer to define a high fluidic resistancestructure (e.g., 2 μm high channels and/or a gap under or over a C− orother structure between the outer channel and culture chamber. A 40 to50 μm SU-8 2050 layer was then spin coated on top of the perfusionchannels. Because the SU-8 2050 is substantially thicker than SU-8 2002,the surface was planarized after spin coating. The cell culture chamberand other channels were then photolithographically defined. PDMS(Sylgard 184, Dow Corning Corporation) was prepared with a 10:1 ratiobetween the base and the curing agents. The PDMS was then poured on the2-level SU8 mold. The mold was degassed in a vacuum chamber for 10 minbefore curing in a 70° C. oven for 4 h.

The device dies were then cut by a razor blade and the fluidicconnection ports were punched using an 18 gauge flat tip needle. Thedevice was then irreversibly bonded to a coverglass (Fisher Scientific)after oxygen plasma treatment (PlasmaTherm Etcher, 50 W, 2 Torr, 40 s)on both the bottom of the device and the glass slide. 20 gauge stainlesssteel connectors (Instech Laboratories) and soft tubings (Cole ParmerCorporation) were used to provide fluidic connections to a syringe pump(Cole Parmer 74900).

In alternative embodiments, (e.g., for the artificial tissuemicrofluidic device) a different fabrication method was used. An example8-unit microfluidic bioreactor chip was manufactured by heterogeneouslyintegrating PMMA reservoirs with PDMS microfluidic devices. The previousdescribed method demonstrate the use of PDMS and soft lithographytechnology for a syringe pump driven cell culture array. For higherthroughput cell-based experimentation, an alternative fabrication methodwas used to “sandwich” PDMS between a PMMA sheet and a glass slide tofacilitate integration with plastic-based materials. In this particularexample, the PDMS is 0.5 mm thick, the PMMA sheet is 1.5 mm thick andthe glass slide is 1 mm thick. The composite PMMA/PDMS microfluidic chipwas then bonded to another piece of PMMA plate containing reagentreservoirs and fluidic connections. FIG. 20 shows the fabricationresults of the 8-unit microfluidic bioreactor chip. The PDMSmicrofluidic features were fabricated using the conventional softlithography technology as described above and the PMMA well plate wascut by a 25W VersaLASER CO₂ laser cutter. Transparent acrylic cement wasthen applied to adhesively bond the PMMA/PDMS composite chip to the PMMAwell plate.

9. Example Operation

Operation of the microfluidic bioreactor chip was accomplished using aninterface platform developed at CellASIC. Each bioreactor chip currentlyprovides 8 independent culture experiments, each with a separate inletand outlet reservoir, and according to specific embodiments of theinvention cell loading can be performed on all eight chamberssimultaneously, significantly saving the biomasses. The standard PMMAwell plate format allowed direct pipetting of cells, culture medium andreagents. The fabrication of the chip also enables visualization of allfluidic flows using standard microscopy or high content screeningmethods. For cell loading and initial priming, a custom built airpressure control manifold is used. Due to the low flow rates necessaryfor medium perfusion (˜5 nl/min), a simple gravity driven flow methodproves to be reliable. In addition, each bioreactor chip can be primedand loaded with cells separately, and then put into an incubator forgravity-driven perfusion on inclined racks.

Example all Plastic Fabrication

In further embodiments, a culture device can also be fabricated with allplastics. FIG. 19 illustrates a CAD drawing of a proposed 96-unit PMMAmicrofluidic bioreactor wherein in this example each well on thebioreactor is SBS standard size (3.5 mm in diameter) and the cellseeding columns are positioned in the center of the drug inlet andperfusate outlet wells; therefore, the bioreactor is compatible withstandard plate readers. In this example, 96 continuous medium cell-basedexperiments can be conducted on a single acrylic plate. Since thebioreactor plate is SBS standard, it is compatible with the existingrobotic liquid handling system and plate reader; therefore, the plateitself can be a modular integration in existing research labs. Tofacilitate high throughput data acquisition, the fluidically trappedcells are positioned in the middle of the drug inlet and the perfusateoutlet wells; therefore, the luminescent or fluorescent signals from thecells can be directly read from a conventional plate reader forcell-based assays.

To fabricate the microfluidic bioreactor plate, a 6 mm thick PMMA sheet(McMaster-Carr) is laser cut (25W CO₂ laser, VersaLASER) or injectionmolded to create a top piece containing all cell inlets, drug inlets andperfusate outlet wells. A hard polymer master template (or siliconmaster template or electroform master template) such as those that canbe fabricated in Berkeley Microfabrication Laboratory, is then hotembossed (Tetrahedron Associates, SPF-8) into a 1.5 mm thick PMMA sheet(McMaster-Carr) to create a bottom piece with microfluidic structures.Other than hot embossing, injection molding can also be an option. Thetop and bottom pieces are then thermally bonded together (TetrahedronAssociates, SPF-8) to complete the microfluidic plate. It is alsopossible to have the microfluidic structures, inlet and outlet wells ona same single piece. FIG. 24 depicts the overall fabrication steps.

Various groups have successfully demonstrated hot embossing of nano- tomicro-sized features using different master templates, as well asthermal bonding between two PMMA sheets; however, CellASIC is the firstone to apply these processes for high throughput cell-basedexperimentations. The key parameters to address are temperature,pressure and time. The major challenge is the deformation of PMMA duringthe bonding process. Because the minimum features in various designsaccording to specific embodiments of the invention, are at micron-scale,the control of temperature in some example fabrication methods iscritical. An alternative approach is to use adhesive bonding by spincoating an adhesive layer at a thickness thinner than any microfluidicdevice features on the plate to prevent blockage of microfluidicchannels.

10. Diagnostic and Drug Development Uses

As described above, following identification and validation of a assayfor a particular cellular process, in specific embodiments devicesand/or systems as described herein are used in clinical or researchsettings, such as to screen possible active compounds, predicativelycategorize subjects into disease-relevant classes, text toxicity ofsubstances, etc. Devices according to the methods the invention can beutilized for a variety of purposes by researchers, physicians,healthcare workers, hospitals, laboratories, patients, companies andother institutions. For example, the devices can be applied to: diagnosedisease; assess severity of disease; predict future occurrence ofdisease; predict future complications of disease; determine diseaseprognosis; evaluate the patient's risk; assess response to current drugtherapy; assess response to current non-pharmacologic therapy; determinethe most appropriate medication or treatment for the patient; anddetermine most appropriate additional diagnostic testing for thepatient, among other clinically and epidemiologically relevantapplications. Essentially any disease, condition, or status for which abiologic culture is useful can be evaluated.

Web Site Embodiment

The methods of this invention can be implemented in a localized ordistributed data environment. For example, in one embodiment featuring alocalized computing environment, a microchamber culture device accordingto specific embodiments of the present invention is configured linked toa computational device equipped with user input and output features. Ina distributed environment, the methods can be implemented on a singlecomputer, a computer with multiple processes or, alternatively, onmultiple computers.

Kits

A device according to specific embodiments of the present invention isoptionally provided to a user as a kit. Typically, a kit of theinvention contains one or more microchamber culture array devicesconstructed according to the methods described herein. Most often, thekit contains a diagnostic sensor packaged in a suitable container. Thekit typically further comprises, one or more additional reagents, e.g.,substrates, tubes and/or other accessories, reagents for collectingblood samples, buffers, e.g., erythrocyte lysis buffer, leukocyte lysisbuffer, hybridization chambers, cover slips, etc., as well as a softwarepackage, e.g., including the statistical methods of the invention, e.g.,as described above, and a password and/or account number for accessingthe compiled database. The kit optionally further comprises aninstruction set or user manual detailing preferred methods of using thekit components for sensing a substance of interest.

When used according to the instructions, the kit enables the user toidentify disease specific cellular processes. The kit can also allow theuser to access a central database server that receives and providesexpression information to the user. Such information facilitates thediscovery of additional diagnostic characteristics by the user.Additionally, or alternatively, the kit allows the user, e.g., a healthcare practitioner, clinical laboratory, or researcher, to determine theprobability that an individual belongs to a clinically relevant class ofsubjects (diagnostic or otherwise). In HTS, a kit according to specificembodiments of the invention can allow a drug developer or clinician todetermine cellular responses to one or more treatments or reagents, fordiagnostic or therapeutic purposes.

Embodiment in a Programmed Information Appliance

The invention may be embodied in whole or in part as a logic or otherdescription for construction of the devices according to specificembodiments of the invention. In such a case, the invention may beembodied in a computer understandable descriptor language, which may beused to create fabricated devices that operate as herein described.

Integrated Systems

Integrated systems for the collection and analysis of cellular and otherdata as well as for the compilation, storage and access of the databasesof the invention, typically include a digital computer with softwareincluding an instruction set for sequence searching and/or analysis,and, optionally, one or more of high-throughput sample control software,image analysis software, collected data interpretation software, arobotic control armature for transferring solutions from a source to adestination (such as a detection device) operably linked to the digitalcomputer, an input device (e.g., a computer keyboard) for enteringsubject data to the digital computer, or to control analysis operationsor high throughput sample transfer by the robotic control armature.Optionally, the integrated system further comprises valves,concentration gradients, fluidic multiplexors and/or other microfluidicstructures for interfacing to a microchamber as described.

Readily available computational hardware resources using standardoperating systems can be employed and modified according to theteachings provided herein, e.g., a PC (Intel x86 or Pentiumchip-compatible DOS,™ OS2,™ WINDOWS,™ WINDOWS NT,™ WINDOWS95,™WINDOWS98,™ LINUX, or even Macintosh, Sun or PCs will suffice) for usein the integrated systems of the invention. Current art in softwaretechnology is adequate to allow implementation of the methods taughtherein on a computer system. Thus, in specific embodiments, the presentinvention can comprise a set of logic instructions (either software, orhardware encoded instructions) for performing one or more of the methodsas taught herein. For example, software for providing the data and/orstatistical analysis can be constructed by one of skill using a standardprogramming language such as Visual Basic, Fortran, Basic, Java, or thelike. Such software can also be constructed utilizing a variety ofstatistical programming languages, toolkits, or libraries.

FIG. 24 is a block diagram showing a representative example logic devicein which various aspects of the present invention may be embodied. FIG.24 shows an information appliance (or digital device) 700 that may beunderstood as a logical apparatus that can read instructions from media717 and/or network port 719, which can optionally be connected to server720 having fixed media 722. Apparatus 700 can thereafter use thoseinstructions to direct server or client logic, as understood in the art,to embody aspects of the invention. One type of logical apparatus thatmay embody the invention is a computer system as illustrated in 700,containing CPU 707, optional input devices 709 and 711, disk drives 715and optional monitor 705. Fixed media 717, or fixed media 722 over port719, may be used to program such a system and may represent a disk-typeoptical or magnetic media, magnetic tape, solid state dynamic or staticmemory, etc. In specific embodiments, the invention may be embodied inwhole or in part as software recorded on this fixed media. Communicationport 719 may also be used to initially receive instructions that areused to program such a system and may represent any type ofcommunication connection.

Various programming methods and algorithms, including genetic algorithmsand neural networks, can be used to perform aspects of the datacollection, correlation, and storage functions, as well as otherdesirable functions, as described herein. In addition, digital or analogsystems such as digital or analog computer systems can control a varietyof other functions such as the display and/or control of input andoutput files. Software for performing the electrical analysis methods ofthe invention are also included in the computer systems of theinvention.

Optionally, the integrated systems of the invention include an automatedworkstation. For example, such a workstation can prepare and analyzesamples by performing a sequence of events including: preparing samplesfrom a tissue or blood sample; placing the samples into a microchamberarray of the invention; and detecting cell or other reactions byoptical, electrical or chemical measurements. The reaction data isdigitized and recorded in the appropriate database.

Automated and/or semi-automated methods for solid and liquid phasehigh-throughput sample preparation and evaluation are available, andsupported by commercially available devices. For example, roboticdevices for preparation of cells. Alternatively, or in addition, roboticsystems for liquid handling are available from a variety of sources,e.g., automated workstations like the automated synthesis apparatusdeveloped by Takeda Chemical Industries, LTD. (Osaka, Japan) and manyrobotic systems utilizing robotic arms (Zymate II, Zymark Corporation,Hopkinton, Mass.; Orca, Beckman Coulter, Inc. (Fullerton, Calif.)) whichmimic the manual operations performed by a scientist. Any of the abovedevices are suitable for use with the present invention, e.g., forhigh-throughput analysis of library components or subject samples. Thenature and implementation of modifications to these devices (if any) sothat they can operate as discussed herein will be apparent to personsskilled in the relevant art.

Other Embodiments

Although the present invention has been described in terms of variousspecific embodiments, it is not intended that the invention be limitedto these embodiments. Modification within the spirit of the inventionwill be apparent to those skilled in the art.

It is understood that the examples and embodiments described herein arefor illustrative purposes and that various modifications or changes inlight thereof will be suggested by the teachings herein to personsskilled in the art and are to be included within the spirit and purviewof this application and scope of the claims.

All publications, patents, and patent applications cited herein or filedwith this submission, including any references filed as part of anInformation Disclosure Statement, are incorporated by reference in theirentirety.

What is claimed:
 1. A method of handling cells, comprising: (a) fluidically preparing sample cells; (b) fluidically transporting said cells through one or more microfluidic channels into one or more micro-sized micro culture units, at least one said unit comprising: (i) a microchamber with a culture area having a culture area inlet, the culture area inlet configured to allow passage of cells or other culture objects into the culture area; and (ii) a flow around channel having a flow channel inlet and a separate flow around channel outlet, the flow around channel inlet, the flow around channel outlet, and the flow around channel separated from the microchamber culture area and the culture area inlet by one or more micro diffusion structures; (c) flowing medium and/or reagents through said flow around channel inlet, channel and outlet; wherein medium and/or reagents in said flow around channel can enter said microchamber and waste can exit said microchamber into said flow around channel by diffusion and/or mass transfer through said micro diffusion structures; and wherein each micro diffusion structure is configured to resist fluidic flow between the flow around channel and the microchamber thereby allowing fluidic mass transport by diffusion without substantially impeding fluidic flow in the flow around channel; and (d) culturing said cells through continuous perfusion of a medium through said micro culture areas.
 2. The method of claim 1, wherein said micro diffusion structures have a fluidic resistance ratio ranging from 10:1 to 30:1.
 3. The method of claim 1, wherein said micro diffusion structures comprise a plurality of micro passages that are arranged as part of a grid, said grid comprising a plurality of intersecting passages that are substantially smaller in cross section than said flow around channel or said microchamber.
 4. The method of claim 1, further comprising: analyzing multiple parameters of one or more cells by fluidically addressing said micro culture areas with one or more compounds and acquiring data regarding cellular responses in said micro culture areas chambers.
 5. The method of claim 4, wherein said acquiring data regarding cellular responses comprises one or more steps selected form the group consisting of: continuously capturing images of said cells in said micro culture areas; continuously measuring the perfusate in said microfluidic channels; and electrically detecting cellular responses in said microchambers.
 6. The method of claim 4, wherein the culturing cells comprises culturing cells in solid aggregates to provide functional artificial tissues and/or organs.
 7. A method of handling cells, comprising: (a) fluidically preparing sample cells; (b) fluidically transporting said cells through one or more microfluidic channels into a plurality of culture units, at least one of said culture units comprising: (i) a microchamber with a culture area having a culture area inlet, the culture area inlet configured to allow passage of cells or other culture objects into the culture area; (ii) a flow channel having a flow channel inlet and a separate flow channel outlet, the flow channel inlet, the flow channel outlet, and the flow channel separated from the microchamber culture area and the culture area inlet by: (1) one or more micro diffusion structures substantially surrounding the microchamber culture area and positioned between the culture area and the flow channel; (2) wherein each micro diffusion structure comprises one or more micro passages providing fluidic connection between the flow channel and the microchamber culture area; and (iii) a detector configured to capture images of said cells in said microchamber; (c) flowing medium and/or reagents through said flow channel inlet, flow channel and outlet; wherein medium and/or reagents in said flow channel can enter said microchamber and waste can exit said microchamber into said flow channel by diffusion and/or mass transfer through said micro diffusion structures; and wherein each micro diffusion structure is configured to resist fluidic flow between the flow around channel and the microchamber thereby allowing fluidic mass transport by diffusion without substantially impeding fluidic flow in the flow channel; and (d) culturing said cells through continuous perfusion of a medium through said micro culture areas.
 8. The method of claim 7, wherein said micro diffusion structures have a high fluidic resistance ratio ranging from 10:1 to 30:1.
 9. The method of claim 7, wherein said micro diffusion structures comprise a plurality of micro passages that are arranged as part of a grid, said grid comprising a plurality of intersecting passages that are substantially smaller in cross section than said flow around channel or said microchamber.
 10. The method of claim 7, further comprising: continuously capturing images of said cells in said microchambers; continuously measuring the perfusate in said microfluidic channels; and electrically detecting cellular responses in said microchambers. 